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RAxML_ONLY-500M2-12.o9561505
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RAxML_ONLY-500M2-12.o9561505
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----------------------------------------
Begin Torque Prologue (Sat Sep 21 17:25:51 2019)
Job ID: 9561505.cc-mgmt1.campuscluster.illinois.edu
Username: binghui2
Group: tallis
Job Name: RAxML_ONLY-500M2-12
Limits: nodes=1:ppn=12,walltime=04:00:00,neednodes=1:ppn=12
Job Queue: secondary
Account: tallis
Nodes: golub101
End Torque Prologue
----------------------------------------
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
RAxML output files with the run ID <bestml> already exist
in directory /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R12/ ...... exiting
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences SBDH and SED are exactly identical
IMPORTANT WARNING
Found 1 sequence that is exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R13/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 4
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2174 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 67.36%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2174
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R13/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R13/ -m GTRGAMMA -T 6 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.252 0.243 0.247 0.258
Inference[0]: Time 1014.086782 GAMMA-based likelihood -429779.921291, best rearrangement setting 10
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -429779.908178 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R13/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -429779.908178 ....
Final GAMMA-based Score of best tree -429779.908178
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R13/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R13/RAxML_bestTree.bestml
Overall execution time: 1242.587338 secs or 0.345163 hours or 0.014382 days
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 5
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2345 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 69.69%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2345
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R14/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R14/ -m GTRGAMMA -T 6 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.261 0.243 0.243 0.254
Inference[0]: Time 1014.954586 GAMMA-based likelihood -422194.339626, best rearrangement setting 10
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -422194.294148 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R14/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -422194.294148 ....
Final GAMMA-based Score of best tree -422194.294148
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R14/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R14/RAxML_bestTree.bestml
Overall execution time: 1261.813644 secs or 0.350504 hours or 0.014604 days
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2018 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 64.45%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2018
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R15/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R15/ -m GTRGAMMA -T 5 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.254 0.248 0.237 0.261
Inference[0]: Time 971.559784 GAMMA-based likelihood -424966.360241, best rearrangement setting 10
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -424966.335306 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R15/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -424966.335306 ....
Final GAMMA-based Score of best tree -424966.335306
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R15/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R15/RAxML_bestTree.bestml
Overall execution time: 1217.257410 secs or 0.338127 hours or 0.014089 days
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences SBHF and SEDB are exactly identical
IMPORTANT WARNING
Found 1 sequence that is exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R16/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 6
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2614 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 74.17%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2614
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R16/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R16/ -m GTRGAMMA -T 7 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.266 0.239 0.239 0.255
Inference[0]: Time 1076.208036 GAMMA-based likelihood -443476.550402, best rearrangement setting 10
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -443476.516805 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R16/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -443476.516805 ....
Final GAMMA-based Score of best tree -443476.516805
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R16/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R16/RAxML_bestTree.bestml
Overall execution time: 1313.551240 secs or 0.364875 hours or 0.015203 days
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences SEIJ and SEBB are exactly identical
IMPORTANT WARNING
Found 1 sequence that is exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R17/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 4
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2135 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 62.18%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2135
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R17/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R17/ -m GTRGAMMA -T 5 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.257 0.244 0.244 0.255
Inference[0]: Time 864.995330 GAMMA-based likelihood -396111.345636, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -396111.316751 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R17/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -396111.316751 ....
Final GAMMA-based Score of best tree -396111.316751
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R17/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R17/RAxML_bestTree.bestml
Overall execution time: 1117.867140 secs or 0.310519 hours or 0.012938 days
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences SCGJ and SDIB are exactly identical
IMPORTANT WARNING
Found 1 sequence that is exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R18/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 4
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2349 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 69.58%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2349
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R18/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R18/ -m GTRGAMMA -T 6 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.252 0.246 0.246 0.256
Inference[0]: Time 1048.650273 GAMMA-based likelihood -443820.507878, best rearrangement setting 10
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -443820.498140 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R18/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -443820.498140 ....
Final GAMMA-based Score of best tree -443820.498140
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R18/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R18/RAxML_bestTree.bestml
Overall execution time: 1305.053150 secs or 0.362515 hours or 0.015105 days
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences SHB and SBDI are exactly identical
IMPORTANT WARNING
Found 1 sequence that is exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R19/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 6
This is RAxML Worker Pthread Number: 1
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 5
This is RAxML Worker Pthread Number: 4
This is RAxML Worker Pthread Number: 3
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2468 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 72.08%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2468
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M2/R19/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R19/ -m GTRGAMMA -T 7 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.250 0.248 0.246 0.256
Inference[0]: Time 674.080532 GAMMA-based likelihood -441827.966206, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -441827.899331 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R19/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -441827.899331 ....
Final GAMMA-based Score of best tree -441827.899331
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R19/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M2/R19/RAxML_bestTree.bestml
Overall execution time: 884.829552 secs or 0.245786 hours or 0.010241 days
----------------------------------------
Begin Torque Epilogue (Sat Sep 21 19:45:03 2019)
Job ID: 9561505.cc-mgmt1.campuscluster.illinois.edu
Username: binghui2
Group: tallis
Job Name: RAxML_ONLY-500M2-12
Session: 75317
Limits: nodes=1:ppn=12,walltime=04:00:00,neednodes=1:ppn=12
Resources: cput=13:52:06,vmem=883656kb,walltime=02:19:12,mem=198456kb,energy_used=0
Job Queue: secondary
Account: tallis
Nodes: golub101
End Torque Epilogue
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